|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: PTX3 |
Gene summary for PTX3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PTX3 | Gene ID | 5806 |
| Gene name | pentraxin 3 | |
| Gene Alias | TNFAIP5 | |
| Cytomap | 3q25.32 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | P26022 |
Top |
Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 5806 | PTX3 | P2T-E | Human | Esophagus | ESCC | 9.12e-40 | 1.14e+00 | 0.1177 |
| 5806 | PTX3 | P5T-E | Human | Esophagus | ESCC | 1.72e-02 | 3.13e-01 | 0.1327 |
| 5806 | PTX3 | P11T-E | Human | Esophagus | ESCC | 7.19e-08 | 1.34e+00 | 0.1426 |
| 5806 | PTX3 | P16T-E | Human | Esophagus | ESCC | 1.04e-15 | 4.70e-01 | 0.1153 |
| 5806 | PTX3 | P32T-E | Human | Esophagus | ESCC | 3.73e-25 | 7.97e-01 | 0.1666 |
| 5806 | PTX3 | P56T-E | Human | Esophagus | ESCC | 1.19e-04 | 8.39e-01 | 0.1613 |
| 5806 | PTX3 | P76T-E | Human | Esophagus | ESCC | 4.06e-15 | 5.05e-01 | 0.1207 |
| 5806 | PTX3 | P83T-E | Human | Esophagus | ESCC | 1.42e-02 | 4.85e-01 | 0.1738 |
| 5806 | PTX3 | ATC09 | Human | Thyroid | ATC | 1.28e-28 | 1.44e+00 | 0.2871 |
| 5806 | PTX3 | ATC11 | Human | Thyroid | ATC | 5.90e-10 | 2.75e+00 | 0.3386 |
| 5806 | PTX3 | ATC12 | Human | Thyroid | ATC | 1.01e-02 | 2.57e-01 | 0.34 |
| 5806 | PTX3 | ATC1 | Human | Thyroid | ATC | 2.56e-30 | 1.50e+00 | 0.2878 |
| 5806 | PTX3 | ATC3 | Human | Thyroid | ATC | 6.82e-19 | 2.48e+00 | 0.338 |
| 5806 | PTX3 | ATC4 | Human | Thyroid | ATC | 8.62e-06 | 3.15e-01 | 0.34 |
| 5806 | PTX3 | ATC5 | Human | Thyroid | ATC | 2.03e-03 | 1.61e-01 | 0.34 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
Top |
Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:0016032111 | Esophagus | ESCC | viral process | 301/8552 | 415/18723 | 3.34e-29 | 1.32e-26 | 301 |
| GO:0019058111 | Esophagus | ESCC | viral life cycle | 226/8552 | 317/18723 | 1.17e-20 | 1.76e-18 | 226 |
| GO:0050792111 | Esophagus | ESCC | regulation of viral process | 119/8552 | 164/18723 | 2.19e-12 | 9.03e-11 | 119 |
| GO:1903900111 | Esophagus | ESCC | regulation of viral life cycle | 106/8552 | 148/18723 | 1.26e-10 | 3.72e-09 | 106 |
| GO:0044403111 | Esophagus | ESCC | biological process involved in symbiotic interaction | 186/8552 | 290/18723 | 1.43e-10 | 4.16e-09 | 186 |
| GO:0051701111 | Esophagus | ESCC | biological process involved in interaction with host | 135/8552 | 203/18723 | 1.49e-09 | 3.49e-08 | 135 |
| GO:0052126111 | Esophagus | ESCC | movement in host environment | 117/8552 | 175/18723 | 1.14e-08 | 2.26e-07 | 117 |
| GO:0061458110 | Esophagus | ESCC | reproductive system development | 247/8552 | 427/18723 | 2.24e-07 | 3.42e-06 | 247 |
| GO:00091002 | Esophagus | ESCC | glycoprotein metabolic process | 226/8552 | 387/18723 | 2.64e-07 | 3.94e-06 | 226 |
| GO:004860818 | Esophagus | ESCC | reproductive structure development | 245/8552 | 424/18723 | 2.82e-07 | 4.14e-06 | 245 |
| GO:004852516 | Esophagus | ESCC | negative regulation of viral process | 66/8552 | 92/18723 | 3.49e-07 | 4.88e-06 | 66 |
| GO:0044409111 | Esophagus | ESCC | entry into host | 96/8552 | 151/18723 | 6.73e-06 | 6.84e-05 | 96 |
| GO:005185115 | Esophagus | ESCC | modulation by host of symbiont process | 43/8552 | 60/18723 | 4.00e-05 | 3.22e-04 | 43 |
| GO:00301984 | Esophagus | ESCC | extracellular matrix organization | 171/8552 | 301/18723 | 6.08e-05 | 4.67e-04 | 171 |
| GO:004671827 | Esophagus | ESCC | viral entry into host cell | 89/8552 | 144/18723 | 6.84e-05 | 5.18e-04 | 89 |
| GO:00430624 | Esophagus | ESCC | extracellular structure organization | 171/8552 | 302/18723 | 7.73e-05 | 5.76e-04 | 171 |
| GO:00452294 | Esophagus | ESCC | external encapsulating structure organization | 172/8552 | 304/18723 | 7.80e-05 | 5.80e-04 | 172 |
| GO:0043903111 | Esophagus | ESCC | regulation of biological process involved in symbiotic interaction | 49/8552 | 72/18723 | 1.03e-04 | 7.26e-04 | 49 |
| GO:005181714 | Esophagus | ESCC | modulation of process of other organism involved in symbiotic interaction | 54/8552 | 81/18723 | 1.09e-04 | 7.64e-04 | 54 |
| GO:0051346110 | Esophagus | ESCC | negative regulation of hydrolase activity | 208/8552 | 379/18723 | 1.76e-04 | 1.14e-03 | 208 |
| Page: 1 2 3 4 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
Top |
Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| Page: 1 |
Top |
Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 |
Top |
Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| PTX3 | SNV | Missense_Mutation | c.647C>T | p.Thr216Ile | p.T216I | P26022 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-BH-A1EV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |
| PTX3 | SNV | Missense_Mutation | novel | c.139T>C | p.Cys47Arg | p.C47R | P26022 | protein_coding | deleterious(0) | possibly_damaging(0.642) | TCGA-EW-A6SA-01 | Breast | breast invasive carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| PTX3 | SNV | Missense_Mutation | c.52N>A | p.Glu18Lys | p.E18K | P26022 | protein_coding | tolerated(0.14) | benign(0.265) | TCGA-UC-A7PF-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| PTX3 | SNV | Missense_Mutation | novel | c.673N>C | p.Phe225Leu | p.F225L | P26022 | protein_coding | tolerated(0.05) | possibly_damaging(0.85) | TCGA-AA-3947-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PTX3 | SNV | Missense_Mutation | c.600N>C | p.Arg200Ser | p.R200S | P26022 | protein_coding | tolerated(0.46) | benign(0.006) | TCGA-AD-A5EJ-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PTX3 | SNV | Missense_Mutation | novel | c.1136N>T | p.Tyr379Phe | p.Y379F | P26022 | protein_coding | tolerated(0.27) | possibly_damaging(0.649) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| PTX3 | SNV | Missense_Mutation | rs765511514 | c.40N>A | p.Ala14Thr | p.A14T | P26022 | protein_coding | tolerated(0.11) | benign(0.035) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PTX3 | SNV | Missense_Mutation | novel | c.947N>T | p.Gly316Val | p.G316V | P26022 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PTX3 | SNV | Missense_Mutation | novel | c.566N>A | p.Ser189Tyr | p.S189Y | P26022 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PTX3 | SNV | Missense_Mutation | novel | c.38C>A | p.Ser13Tyr | p.S13Y | P26022 | protein_coding | tolerated(0.15) | benign(0.233) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
| Page: 1 2 3 |
Top |
Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| Page: 1 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |